A. Field of the Invention
1. The present invention relates to a computer-based system, methods and graphical interface which integrates capabilities for graphical information and data storage, modeling, and simulation of complex systems, and which modularizes the information and data in a hierarchy of organized sets of composite icons comprising: phase icons, representing discrete time compartments and location icons, representing discrete space compartments, which in turn contain sets of reservoir icons, representing pools of entities, process icons, representing processes where the entities participate, and entity icons, representing the description of the entities. In addition, the phase icons, reservoir icons, and process icons comprise a set of quantitative variables and parameters, and a set of associated methods that permit real-time simulations of the graphic models created with those modular components. The graphical interface further provides quick access to several automated methods for compiling, retrieving, and displaying the modular components of the graphic models and their contained information and data.
B. Related Applications
1. This application is related to the patent entitled "Computer-Based System, Methods and Graphical Interface for Information Storage, Modeling and Simulation of Complex Systems" invented by the same inventor and filed with this application in the United States Patent and Trademark Office with Ser. No. 08/373,992. This application is incorporated here by this reference.
C. Brief Description of a Modeling and Simulation System for Chemical Pathways
1. The computer-based system object of this invention is implemented as an application developed on top of the computer-based system object of the accompanying patent filing with Ser. No. 08/373,992. Therefore, the system, methods and graphical interface object of this invention are an extension of the system, methods and graphical interface described in detail in the accompanying patent filing , which are here included by reference, and which will not be here repeated unless modifications are introduced. In some cases, alternative implementations are included. The object of the accompanying filing is a system for graphical information and data storage, modeling, and simulation of complex systems, and more in particular of complex systems in the chemical domain, with the implementation focusing on modeling of the mechanisms and the overall architecture of chemical and biochemical pathways, and the simulation of the kinetics of those pathways. The current invention adds two levels of complexity to such system by adding the dimensions of time and space, allowing to model even more complex systems. The current embodiment of this invention graphically models higher levels of complexity represented by complex cellular systems, and it is based on the system, methods and graphical interface already described, and on additional innovative systems, methods and graphical interfaces which are innovative teachings of the present invention. The reader is advised to read said accompanying patent filing for the details of the system already described, which in conjunction with the present filing provides a complete description of the system, methods and interface of this invention . Here we will mainly refer to those new aspects that refer to the higher complexity, and to additional searching capabilities that have been added to take advantage of the knowledge contained in the architecture of the system.
2. This system integrates a variety of forms of knowledge representation, some of them totally novel, while some of these forms may have been given a previous treatment by other authors which may be similar in some of its aspects to the treatment given in the current embodiment of this invention. However, upon integration into a totally new approach, that treatment becomes a part of a novel representation and innovative system. For example, regarding the semi-quantitative simulation component, which is just one of several applications offered by the system object of this invention, L. E. Widman (1991) describes a semi-quantitative simulation of dynamic systems in a totally different domain. What both systems have in common is the assumption that, as stated by Widman: "a semi-quantitative model . . . is intended to predict correctly the direction in which each variable will change and to provide a correct partial ordering of the magnitude of change relative to other variables in the model. . . . The questions can be answered in terms of relative quantities rather than absolute quantities. . . . model parameters that are not specified explicitly are given the implicit, default values of `normal` (unity) . . . ". Similar but different concepts are applied in developing part of the system of this invention, but as it will become clear from the detail descriptions in the following sections, not only are they applied to a new domain, but the innovative tools and methods used in the present implementation are also quite different. For example, while he assumes that ". . . the default, or implicit, value of `normal` maps onto unity for parameters and onto zero for variables . . . " the assumption in the prebuilt modular components in the current implementation differs from that statement in that the default, or implicit, value of `normal` may map onto values other than unity for parameters and onto values other than zero for variables, with those values being defined based on expert knowledge.